Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach

Abstract

The heterogeneous and chaotic nature of osteosarcoma has confounded accurate molecular classification, prognosis, and prediction for this tumor. The occurrence of spontaneous osteosarcoma is largely confined to humans and dogs. While the clinical features are remarkably similar in both species, the organization of dogs into defined breeds provides a more homogeneous genetic background that may increase the likelihood to uncover molecular subtypes for this complex disease. We thus hypothesized that molecular profiles derived from canine osteosarcoma would aid in molecular subclassification of this disease when applied to humans. To test the hypothesis, we performed genome wide gene expression profiling in a cohort of dogs with osteosarcoma, primarily from high-risk breeds. To further reduce inter-sample heterogeneity, we assessed tumor-intrinsic properties through use of an extensive panel of osteosarcoma-derived cell lines. We observed strong differential gene expression that segregated samples into two groups with differential survival probabilities. Groupings were characterized by the inversely correlated expression of genes associated with G2/M transition and DNA damage checkpoint and microenvironment-interaction categories. This signature was preserved in data from whole tumor samples of three independent dog osteosarcoma cohorts, with stratification into the two expected groups. Significantly, this restricted signature partially overlapped a previously defined, predictive signature for soft tissue sarcomas, and it unmasked orthologous molecular subtypes and their corresponding natural histories in five independent data sets from human patients with osteosarcoma. Our results indicate that the narrower genetic diversity of dogs can be utilized to group complex human osteosarcoma into biologically and clinically relevant molecular subtypes. This in turn may enhance prognosis and prediction, and identify relevant therapeutic targets.

Aberrant Retinoblastoma (RB)-E2F Transcriptional Regulation Defines Molecular Phenotypes of Osteosarcoma

“…Cell Lines and Cell Culture-Canine and human osteosarcoma cell lines and the Jurkat T-cell leukemia line were established and maintained as previously described (5,16,17). OSCA-8, OSCA-32, and OSCA-40 cells were modified to stably express GFP and firefly luciferase (Luc) for in vivo experiments (18).…”

“…Gene Expression Profiling-Hybridization to canine 4 ϫ 44, 000 microarray chips (Agilent Technologies, Santa Clara, CA) was done as described at the University of Minnesota Genomics Center (5,18). Probe signal levels were quantile-normalized and summarized as previously described (5) (data archive submitted to the Gene Expression Omnibus).…”

“…In the past decade, the molecular basis of osteosarcoma has received significant attention, and a number of recurring chromosomal aberrations and changes in gene expression have been identified (1)(2)(3)(4)(5). However, these findings have not yet translated into significant improvements in disease prognosis or outcome (2, 6 -8), placing osteosarcoma among the "most wanted" for new and effective therapies (9).…”

“…Previously, we identified a gene signature consisting of ϳ250 genes that stratified canine osteosarcoma into subgroups predictive of patient outcome (5,13). The gene signature and its prognostic value were conserved in tumors from human osteosarcoma patients (5). Tumors from patients with longer survival (henceforth called "molecular phenotype 1") were characterized by decreased expression of genes associated with G 2 /M transition and DNA damage-induced cell cycle checkpoints.…”

“…The conservation of disease mechanisms between canine and human osteosarcoma supports using the former as a comparative model to achieve this goal (2, 5, 10 -12). Previously, we identified a gene signature consisting of ϳ250 genes that stratified canine osteosarcoma into subgroups predictive of patient outcome (5,13). The gene signature and its prognostic value were conserved in tumors from human osteosarcoma patients (5).…”